DOCSLIB.ORG

Metagenome-Assembled Genomes Provide New Insights Into Two

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Metagenome-Assembled Genomes Provide New Insights Into Two bioRxiv preprint doi: https://doi.org/10.1101/392308; this version posted August 15, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 There and back again: metagenome-assembled genomes provide new insights 2 into two thermal pools in Kamchatka, Russia 3 4 Authors: Laetitia G. E. Wilkins1,2#*, Cassandra L. Ettinger2#, Guillaume Jospin2 & 5 Jonathan A. Eisen2,3,4 6 7 Affiliations 8 9 1. Department of Environmental Sciences, Policy & Management, University of 10 California, Berkeley, CA, USA. 11 2. Genome Center, University of California, Davis, CA, USA. 12 3. Department of Evolution and Ecology, University of California, Davis, CA, USA. 13 4. Department of Medical Microbiology and Immunology, University of California, Davis, 14 CA, USA. 15 16 # These authors contributed equally 17 18 *Corresponding author: Laetitia G. E. Wilkins, [email protected], +1-510- 19 643-9688, 304-306 Mulford Hall, University of California, Berkeley, CA, 94720, USA 1 bioRxiv preprint doi: https://doi.org/10.1101/392308; this version posted August 15, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 20 Abstract: 21 22 Culture-independent methods have contributed substantially to our understanding of 23 global microbial diversity. Recently developed algorithms to construct whole genomes 24 from environmental samples have further refined, corrected and revolutionized the tree 25 of life. Here, we assembled draft metagenome-assembled genomes (MAGs) from 26 environmental DNA extracted from two hot springs within an active volcanic ecosystem 27 on the Kamchatka peninsula, Russia. This hydrothermal system has been intensively 28 studied previously with regard to geochemistry, chemoautotrophy, microbial isolation, 29 and microbial diversity. Using a shotgun metagenomics approach, we assembled 30 population-level genomes of bacteria and archaea from two pools using DNA that had 31 previously been characterized via 16S rRNA gene clone libraries. We recovered 36 32 MAGs, 29 of medium to high quality, and placed them in the context of the current 33 microbial tree of life. We highlight MAGs representing previously underrepresented 34 archaeal phyla (Korarchaeota, Bathyarchaeota and Aciduliprofundum) and one 35 potentially new species within the bacterial genus Sulfurihydrogenibium. Putative 36 functions in both pools were compared and are discussed in the context of their 37 diverging geochemistry. This study can be considered complementary to foregoing 38 studies in the same ecosystem as it adds more comprehensive information about 39 phylogenetic diversity and functional potential within this highly selective habitat. 40 41 Keywords: Archaea, hydrothermal, Kamchatka, metagenomics, metagenome- 42 assembled genomes, terrestrial hot springs, tree of life, Uzon Caldera 43 44 Introduction: 45 46 Terrestrial hydrothermal systems are of great interest to the general public and to 47 scientists alike due to their unique and extreme conditions. Hot springs have been 48 sought out by geochemists, astrobiologists and microbiologists around the globe who 49 are interested in their chemical properties, which provide a strong selective pressure on 50 local microorganisms. Drivers of microbial community composition in these springs 2 bioRxiv preprint doi: https://doi.org/10.1101/392308; this version posted August 15, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 51 include temperature, pH, in-situ chemistry, and biogeography 1–3. The heated water 52 streams contain substantial concentrations of carbon dioxide, nitrogen, hydrogen, and 53 hydrogen sulphide. Moreover, high temperature subterranean erosion processes can 54 result in high levels of soluble metals and metalloids. Microbial communities have not 55 only developed strategies to resist these limiting conditions but have also invented ways 56 to thrive by converting hot spring chemicals into energy 4. 57 58 The Uzon Caldera is part of the Pacific Ring of Fire and is one of the largest active 59 volcanic ecosystems in the world 4. The geochemical properties of this system have 60 been studied in detail 5–7. The systematic study of Kamchatka thermophilic microbial 61 communities was initiated by Georgy Zavarzin in the early 1980’s 8. Briefly, the Uzon 62 Caldera was created by a volcanic eruption. It is characterized by high water 63 temperatures (20 - 95° Celsius), a wide range of pH (3.1 - 9.8), and many small lakes 64 that are filled with sediment and pumice, dacite extrusions, and peatbog deposits 9,10. 65 Most of the hydrothermal springs lack dissolved oxygen, but harbour sulphides and rare 66 trace elements (antimony, arsenic, boron, copper, lithium, and mercury 11). Many 67 previously undiscovered bacteria have been isolated in this region using culture- 68 dependent methods 12–14, and 16S rRNA gene amplicon sequencing has revealed a 69 diverse collection of new lineages of archaea 15,16. Although microorganisms from Uzon 70 Caldera are well represented in culture collections 17, this region has remained relatively 71 under-sampled by culture-independent methods 8,9,11,18–23. 72 73 In this study, we focus on two hydrothermal pools, Arkashin Schurf and Zavarzin Spring 74 in the Uzon Caldera that were previously characterized using 16S ribosomal RNA gene 75 sequencing and geochemical analysis by Burgess et al. 9 (Fig. 1). Arkashin Schurf 76 (ARK) is an artificial pool, approximately 1 m2 in size, in the central sector of the East 77 Thermal Field (54°30′0′′ N, 160°0′20′′ E), which was dug during a prospecting expedition 78 to Uzon by Arkadiy Loginov 10. ARK has been generally stable in size and shape since 79 its creation 24. Flocs ranging in colour from pale yellow-orange to bright orange-red have 80 been observed floating in ARK 10. This pool is characterized by high concentrations of 81 arsenic and sulphur, which result from the oxidation and cooling of magmatic waters as 3 bioRxiv preprint doi: https://doi.org/10.1101/392308; this version posted August 15, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 82 they reach the surface of the caldera 9. Zavarzin Spring (ZAV) is a natural pool, 83 approximately 10 m2 in size, in the Eastern Thermal Field (54°29′53′′ N, 160°0′52′′ E). 84 Unlike ARK, the size and shape of ZAV is constantly in flux as vents collapse and 85 emerge and as the amount of snowmelt changes 24. Green microbial mats have been 86 observed around the edge of ZAV and thicker brown and green mats have been found 87 within the pool itself 10. 88 89 Burgess et al. 9 found that the two pools differed geochemically with ARK containing 90 higher amounts of total arsenic, rubidium, calcium, and caesium; and ZAV containing 91 higher amounts of total vanadium, manganese, copper, zinc, strontium, barium, iron and 92 sulphur 10. Water temperatures in ARK ranged from 65°C near the vent to 32°C at the 93 edge of the pool with temperatures as high as 99°C at 10 cm depth into the vent 94 sediments. ZAV showed relatively lower temperatures between 26°C and 74°C at 95 different locations of the pool. 96 97 Using the same DNA that had been used in the Burgess et al. study 9 as our starting 98 material, we applied a metagenomic whole genome shotgun sequencing approach. We 99 binned reads from the environment into individual population-specific genomes and then 100 identified and annotated taxonomic and functional genes for the microorganisms in the 101 two pools. In contrast to the 16S rRNA gene amplicon approach, metagenomic 102 sequencing avoids taxonomic primer bias 25, provides more direct functional prediction 103 information about the system 26, and ultimately can result in a more precise taxonomy 104 through multi-gene and whole-genome phylogenetic approaches 27. However, at low 105 sequencing depths, metagenomic sequencing and whole genome binning capture only 106 the most abundant bacterial genes in the pools. Accordingly, we tested the following 107 questions: (1) Can we recover metagenome-assembled genomes (MAGs) from the two 108 pools? Are there any previously undiscovered or unobserved taxa that can be described 109 using this approach? (2) How do any identified MAGs compare to Burgess et al.’s 110 survey of the microbes in these pools? Do we find any archaea in the ARK pool from 111 which Burgess et al. were unable to amplify any 16S rRNA gene sequences? (3) How 112 do any MAGs found here fit into the current microbial tree of life? (4) Can we identify 4 bioRxiv preprint doi: https://doi.org/10.1101/392308; this version posted August 15, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 113 any differences in the functional genes or specific MAGs between the two pools that 114 might be explained by their diverging geochemistry? 115 116 Results: 117 118 Quality filtering and assembly 119 120 DNA libraries were prepared and then sequenced using Solexa3 84 bp paired-end 121 sequencing.
Load more

Recommended publications
  • Lake Sediment Microbial Communities in the Anthropocene
    Lake sediment microbial communities in the Anthropocene Matti Olavi Ruuskanen A thesis submitted in partial fulfillment of the requirements for the Doctorate in Philosophy degree in Biology with Specialization in Chemical and Environmental Toxicology Department of Biology Faculty of Science University of Ottawa © Matti Olavi Ruuskanen, Ottawa, Canada, 2019 Abstract Since the Industrial Revolution at the end of the 18th century, anthropogenic changes in the environment have shifted from the local to the global scale. Even remote environments such as the high Arctic are vulnerable to the effects of climate change. Similarly, anthropogenic mercury (Hg) has had a global reach because of atmospheric transport and deposition far from emission point sources. Whereas some effects of climate change are visible through melting permafrost, or toxic effects of Hg at higher trophic levels, the often-invisible changes in microbial community structures and functions have received much less attention. With recent and drastic warming- related changes in Arctic watersheds, previously uncharacterized phylogenetic and functional diversity in the sediment communities might be lost forever. The main objectives of my thesis were to uncover how microbial community structure, functional potential and the evolution of mercury specific functions in lake sediments in northern latitudes (>54ºN) are affected by increasing temperatures and Hg deposition. To address these questions, I examined environmental DNA from sediment core samples and high-throughput sequencing to reconstruct the community composition, functional potential, and evolutionary responses to historical Hg loading. In my thesis I show that the microbial community in Lake Hazen (NU, Canada) sediments is structured by redox gradients and pH. Furthermore, the microbes in this phylogenetically diverse community contain genomic features which might represent adaptations to the cold and oligotrophic conditions.
    [Show full text]
  • Phylogeny of Bacterial and Archaeal Genomes Using Conserved Genes: Supertrees and Supermatrices
    Phylogeny of Bacterial and Archaeal Genomes Using Conserved Genes: Supertrees and Supermatrices Jenna Morgan Lang1,2, Aaron E. Darling1, Jonathan A. Eisen1,2* 1 Department of Medical Microbiology and Immunology and Department of Evolution and Ecology, University of California Davis, Davis, California, United States of America, 2 Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America Abstract Over 3000 microbial (bacterial and archaeal) genomes have been made publically available to date, providing an unprecedented opportunity to examine evolutionary genomic trends and offering valuable reference data for a variety of other studies such as metagenomics. The utility of these genome sequences is greatly enhanced when we have an understanding of how they are phylogenetically related to each other. Therefore, we here describe our efforts to reconstruct the phylogeny of all available bacterial and archaeal genomes. We identified 24, single-copy, ubiquitous genes suitable for this phylogenetic analysis. We used two approaches to combine the data for the 24 genes. First, we concatenated alignments of all genes into a single alignment from which a Maximum Likelihood (ML) tree was inferred using RAxML. Second, we used a relatively new approach to combining gene data, Bayesian Concordance Analysis (BCA), as implemented in the BUCKy software, in which the results of 24 single-gene phylogenetic analyses are used to generate a ‘‘primary concordance’’ tree. A comparison of the concatenated ML tree and the primary concordance (BUCKy) tree reveals that the two approaches give similar results, relative to a phylogenetic tree inferred from the 16S rRNA gene. After comparing the results and the methods used, we conclude that the current best approach for generating a single phylogenetic tree, suitable for use as a reference phylogeny for comparative analyses, is to perform a maximum likelihood analysis of a concatenated alignment of conserved, single-copy genes.
    [Show full text]
  • Microbial Distribution in Different Spatial Positions Within the Walls of a Black Sulfide Hydrothermal Chimney
    Vol. 508: 67–85, 2014 MARINE ECOLOGY PROGRESS SERIES Published August 4 doi: 10.3354/meps10841 Mar Ecol Prog Ser Microbial distribution in different spatial positions within the walls of a black sulfide hydrothermal chimney Jiangtao Li1, Huaiyang Zhou1,*, Jiasong Fang1,2,*, Yannan Sun1, Shamik Dasgupta1 1State Key Laboratory of Marine Geology, Tongji University, Shanghai 200092, PR China 2Department of Natural Sciences, Hawaii Pacific University, Kaneohe, Hawaii 96744, USA ABSTRACT: Deep-sea hydrothermal chimneys encompass diverse niches for different micro- bial communities with steep environmental gradients. An active sulfide hydrothermal structure was recovered from the Dudley site of the Main Endeavour Field in the Juan de Fuca Ridge. Subsamples were taken from different spatial positions within the chimney wall and analyzed for mineral composition and microbial biomass and community structure to illustrate the char- acteristics of microbial distribution and environmental constraints. Mineral analysis showed that the chimney was mainly composed of various Fe-, Zn-, and Cu-rich sulfides, with mineral composition and abundance varying with spatial position. Microbial populations in the chimney predominantly consisted of archaeal members affiliated with the deep-sea hydrothermal vent Euryarchaeota group, Thermococcales, and Desulfurococcales, as well as bacterial members of the Gamma-, Epsilon-, and Deltaproteobacteria. Microbial biomass and composition shifted dramatically and formed different microbial zones within the chimney walls, from predomi- nantly mesophilic, sulfur-oxidizing bacterial communities at the outer surfaces to thermophilic or hyperthermophilic, archaeal sulfur-reducers in the inner layers of the chimney. Based on microbial physiological characteristics and their distribution profiles, we inferred that tempera- ture, fluid geochemistry, and organic compounds probably play an important role in selecting for and sustaining microbial communities.
    [Show full text]
  • Metagenome-Assembled Genomes Provide New Insights Into
    bioRxiv preprint doi: https://doi.org/10.1101/392308; this version posted August 15, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 There and back again: metagenome-assembled genomes provide new insights 2 into two thermal pools in Kamchatka, Russia 3 4 Authors: Laetitia G. E. Wilkins1,2#*, Cassandra L. Ettinger2#, Guillaume Jospin2 & 5 Jonathan A. Eisen2,3,4 6 7 Affiliations 8 9 1. Department of Environmental Sciences, Policy & Management, University of 10 California, Berkeley, CA, USA. 11 2. Genome Center, University of California, Davis, CA, USA. 12 3. Department of Evolution and Ecology, University of California, Davis, CA, USA. 13 4. Department of Medical Microbiology and Immunology, University of California, Davis, 14 CA, USA. 15 16 # These authors contributed equally 17 18 *Corresponding author: Laetitia G. E. Wilkins, [email protected], +1-510- 19 643-9688, 304-306 Mulford Hall, University of California, Berkeley, CA, 94720, USA 1 bioRxiv preprint doi: https://doi.org/10.1101/392308; this version posted August 15, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 20 Abstract: 21 22 Culture-independent methods have contributed substantially to our understanding of 23 global microbial diversity.
    [Show full text]
  • Metagenome-Assembled Genomes Provide New Insight Into The
    www.nature.com/scientificreports Corrected: Author Correction OPEN Metagenome-assembled genomes provide new insight into the microbial diversity of two thermal Received: 17 August 2018 Accepted: 17 January 2019 pools in Kamchatka, Russia Published online: 28 February 2019 Laetitia G. E. Wilkins1,2, Cassandra L. Ettinger 2, Guillaume Jospin2 & Jonathan A. Eisen 2,3,4 Culture-independent methods have contributed substantially to our understanding of global microbial diversity. Recently developed algorithms to construct whole genomes from environmental samples have further refned, corrected and revolutionized understanding of the tree of life. Here, we assembled draft metagenome-assembled genomes (MAGs) from environmental DNA extracted from two hot springs within an active volcanic ecosystem on the Kamchatka peninsula, Russia. This hydrothermal system has been intensively studied previously with regard to geochemistry, chemoautotrophy, microbial isolation, and microbial diversity. We assembled genomes of bacteria and archaea using DNA that had previously been characterized via 16S rRNA gene clone libraries. We recovered 36 MAGs, 29 of medium to high quality, and inferred their placement in a phylogenetic tree consisting of 3,240 publicly available microbial genomes. We highlight MAGs that were taxonomically assigned to groups previously underrepresented in available genome data. This includes several archaea (Korarchaeota, Bathyarchaeota and Aciduliprofundum) and one potentially new species within the bacterial genus Sulfurihydrogenibium. Putative functions in both pools were compared and are discussed in the context of their diverging geochemistry. This study adds comprehensive information about phylogenetic diversity and functional potential within two hot springs in the caldera of Kamchatka. Terrestrial hydrothermal systems are of great interest to the general public and to scientists alike due to their unique and extreme conditions.
    [Show full text]
  • Metagenome-Assembled Genomes Provide New Insights Into
    bioRxiv preprint doi: https://doi.org/10.1101/392308; this version posted August 15, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 There and back again: metagenome-assembled genomes provide new insights 2 into two thermal pools in Kamchatka, Russia 3 4 Authors: Laetitia G. E. Wilkins1,2#*, Cassandra L. Ettinger2#, Guillaume Jospin2 & 5 Jonathan A. Eisen2,3,4 6 7 Affiliations 8 9 1. Department of Environmental Sciences, Policy & Management, University of 10 California, Berkeley, CA, USA. 11 2. Genome Center, University of California, Davis, CA, USA. 12 3. Department of Evolution and Ecology, University of California, Davis, CA, USA. 13 4. Department of Medical Microbiology and Immunology, University of California, Davis, 14 CA, USA. 15 16 # These authors contributed equally 17 18 *Corresponding author: Laetitia G. E. Wilkins, [email protected], +1-510- 19 643-9688, 304-306 Mulford Hall, University of California, Berkeley, CA, 94720, USA 1 bioRxiv preprint doi: https://doi.org/10.1101/392308; this version posted August 15, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 20 Abstract: 21 22 Culture-independent methods have contributed substantially to our understanding of 23 global microbial diversity.
    [Show full text]
  • Microbial Communities and Interactions of Nitrogen Oxides with Methanogenesis in Diverse Peatlands of the Amazon Basin
    Supplementary Material Microbial Communities and Interactions of Nitrogen Oxides With Methanogenesis in Diverse Peatlands of the Amazon Basin S. Buessecker, Z. Zamora, A. F. Sarno, D. R. Finn, A. M. Hoyt, J. van Haren, J. D. Urquiza Muñoz, and H. Cadillo-Quiroz Correspondence to: H. Cadillo-Quiroz ([email protected]) Supplementary Material 1 Supplementary Discussion Dissolved organic carbon (DOC) profiles. DOC has emerged as an important predictor of CH4 production in wetland soils (Liu et al., 2012; Morrissey et al., 2013). In comparison, DOC concentrations obtained in this study are at the lower end of values previously reported from Borneo peats (Gandois et al., 2014). All concentration profiles appear stable along soil depth with no indication of sinks. These would conceivably occur in more shallow regions where the fraction of refractory soil carbon is less prevalent (Artz et al., 2006). A DOC sink due to mineralization is not present based on our data. The DOC pool is comprised of diverse organic molecules characterized by a wide molecular size range, organic acids, humic substances of different aromaticities, and protein groups. These compounds may vary with depth even though the bulk concentration may be stagnant. Extracellular enzymes and humic substances may play a crucial role in diverting electron flow from methanogenesis, given the thermodynamic preference over CO2 (Heitmann et al., 2007; Knorr and Blodau, 2009), that would ultimately suppress CH4 production. Based on our results, we can exclude fluctuations of the total DOC pool to have major effects on carbon mineralization in distinct soil layers, but organic compounds could structurally differ along depth and impact specific microbial activities.
    [Show full text]
  • Inter-Domain Microbial Diversity Within the Coral Holobiont Siderastrea Siderea from Two Depth Habitats
    Inter-domain microbial diversity within the coral holobiont Siderastrea siderea from two depth habitats Guido Bonthond1,2, Daniel G. Merselis1,*, Katherine E. Dougan1,*, Trevor Graff3, William Todd3, James W. Fourqurean1 and Mauricio Rodriguez-Lanetty1 1 Department of Biological Sciences, Florida International University, Miami, FL, USA 2 Aquatic Microbiology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands 3 NASA Johnson Space Center, Houston, TX, USA * These authors contributed equally to this work. ABSTRACT Corals host diverse microbial communities that are involved in acclimatization, pathogen defense, and nutrient cycling. Surveys of coral-associated microbes have been particularly directed toward Symbiodinium and bacteria. However, a holistic understanding of the total microbiome has been hindered by a lack of analyses bridging taxonomically disparate groups. Using high-throughput amplicon sequencing, we simultaneously characterized the Symbiodinium, bacterial, and fungal communities associated with the Caribbean coral Siderastrea siderea collected from two depths (17 and 27 m) on Conch reef in the Florida Keys. S. siderea hosted an exceptionally diverse Symbiodinium community, structured differently between sampled depth habitats. While dominated at 27 m by a Symbiodinium belonging to clade C, at 17 m S. siderea primarily hosted a mixture of clade B types. Most fungal operational taxonomic units were distantly related to available reference sequences, indicating the presence of a high degree of fungal novelty within the S. siderea holobiont and a lack of knowledge on the diversity of fungi on coral reefs. Network Submitted 16 August 2017 analysis showed that co-occurrence patterns in the S. siderea holobiont were Accepted 13 January 2018 prevalent among bacteria, however, also detected between fungi and bacteria.
    [Show full text]
  • Microbial Communities and Sulfate-Reducing Microorganisms
    Microbial Communities and Sulfate-Reducing Microorganisms Abundance and Diversity in Municipal Anaerobic Sewage Sludge Digesters from a Wastewater Treatment Plant (Marrakech, Morocco) Abdelaziz Houari, Magali Ranchou-Peyruse, Anthony Ranchou-Peyruse, Rhizlane Bennisse, Radia Bouterfas, Maria Goni, Abdel-Ilah Qatibi, Remy Guyoneaud To cite this version: Abdelaziz Houari, Magali Ranchou-Peyruse, Anthony Ranchou-Peyruse, Rhizlane Bennisse, Radia Bouterfas, et al.. Microbial Communities and Sulfate-Reducing Microorganisms Abundance and Di- versity in Municipal Anaerobic Sewage Sludge Digesters from a Wastewater Treatment Plant (Mar- rakech, Morocco). Processes, MDPI, 2020, 8 (10), pp.1284. 10.3390/pr8101284. hal-02985369 HAL Id: hal-02985369 https://hal.archives-ouvertes.fr/hal-02985369 Submitted on 2 Nov 2020 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. processes Article Microbial Communities and Sulfate-Reducing Microorganisms Abundance and Diversity in Municipal Anaerobic Sewage Sludge Digesters from a Wastewater Treatment Plant (Marrakech, Morocco)
    [Show full text]
  • Genome Sequence of Desulfurella Amilsii Strain TR1 and Comparative Genomics of Desulfurellaceae Family
    fmicb-08-00222 February 20, 2017 Time: 15:42 # 1 ORIGINAL RESEARCH published: 20 February 2017 doi: 10.3389/fmicb.2017.00222 Genome Sequence of Desulfurella amilsii Strain TR1 and Comparative Genomics of Desulfurellaceae Family Anna P. Florentino1,2, Alfons J. M. Stams1,3 and Irene Sánchez-Andrea1* 1 Laboratory of Microbiology, Wageningen University, Wageningen, Netherlands, 2 Sub-department of Environmental Technology, Wageningen University, Wageningen, Netherlands, 3 Centre of Biological Engineering, University of Minho, Braga, Portugal The acidotolerant sulfur reducer Desulfurella amilsii was isolated from sediments of Tinto River, an extremely acidic environment. Its ability to grow in a broad range of pH and to tolerate certain heavy metals offers potential for metal recovery processes. Here we report its high-quality draft genome sequence and compare it to the available genome sequences of other members of Desulfurellaceae family: D. acetivorans, D. multipotens, Hippea maritima, H. alviniae, H. medeae, and H. jasoniae. For most species, pairwise comparisons for average nucleotide identity (ANI) and in silico DNA–DNA hybridization (DDH) revealed ANI values from 67.5 to 80% and DDH values from 12.9 to 24.2%. Edited by: D. acetivorans and D. multipotens, however, surpassed the estimated thresholds of Axel Schippers, Federal Institute for Geosciences species definition for both DDH (98.6%) and ANI (88.1%). Therefore, they should be and Natural Resources, Germany merged to a single species. Comparative analysis of Desulfurellaceae genomes revealed Reviewed by: different gene content for sulfur respiration between Desulfurella and Hippea species. Mario A. Vera, Sulfur reductase is only encoded in D. amilsii, in which it is suggested to play a role in Pontifical Catholic University of Chile, Chile sulfur respiration, especially at low pH.
    [Show full text]
  • By Rabiya Shahid a Thesis Submitted in Partial Fulfillment for the Degree of Master of Science
    CAPITAL UNIVERSITY OF SCIENCE AND TECHNOLOGY, ISLAMABAD New Players in the Sulfur Cycle the Microbial Ecology of Anaerobic and Archaeal Sulfur Reduction; A Step Towards Efficient Microbial Enhanced Oil Recovery by Rabiya Shahid A thesis submitted in partial fulfillment for the degree of Master of Science in the Faculty of Health and Life Sciences Department of Bioinformatics and Biosciences 2020 i Copyright © 2020 by Rabiya Shahid All rights reserved. No part of this thesis June be reproduced, distributed, or transmitted in any form or by any means, including photocopying, recording, or other electronic or mechanical methods, by any information storage and retrieval system without the prior written permission of the author. ii Dedicated to Allah Almighty, Hazrat Muhammad (SAW) and my Parents whose utter support and sheer trust help me to achieve this. CERTIFICATE OF APPROVAL New Players in the Sulfur Cycle the Microbial Ecology of Anaerobic and Archaeal Sulfur Reduction; A Step Towards Efficient Microbial Enhanced Oil Recovery by Rabiya Shahid (MBS181002) THESIS EXAMINING COMMITTEE S. No. Examiner Name Organization (a) External Examiner Dr. Syed Babar Jamal Bacha NUMS, Rawalpindi (b) Internal Examiner Dr. Erum Dilshad CUST, Islamabad (c) Supervisor Dr. Arshia Amin Butt CUST, Islamabad Dr. Arshia Amin Butt Thesis Supervisor June, 2020 Dr. Sahar Fazal Dr. Muhammad Abdul Qadir Head Dean Dept. of Biosciences & Bioinformatics Faculty of Health & Life Sciences June, 2020 June, 2020 iv Author's Declaration I, Rabiya Shahid hereby state that my MS thesis titled \New Players in the Sulfur Cycle the Microbial Ecology of Anaerobic and Archaeal Sulfur Reduction; A Step Towards Efficient Microbial Enhanced Oil Recovery" is my own work and has not been submitted previously by me for taking any degree from Capital University of Science and Technology, Islamabad or anywhere else in the country/abroad.
    [Show full text]
  • Molecular Ecology of Free-Living Chemoautotrophic Microbial Communities at a Shallow-Sea Hydrothermal Vent
    Molecular Ecology of Free-Living Chemoautotrophic Microbial Communities at a Shallow-sea Hydrothermal Vent (Molekulare Ökologie von freilebenden chemoautotrophen mikrobiellen Gemeinschaften an einer Flachwasserhydrothermalquelle) Dissertation Zur Erlangung des Grades eines Doktors der Naturwissenschaften - Dr. rer. nat.- Dem Fachbereich Biologie/Chemie der Universität Bremen vorgelegt von Chia-I Huang Bremen Februar 2012 Die vorliegende Arbeit wurde in der Zeit von Oktober 2008 bis Februar 2012 am Max-Planck- Institut für Marine Mikrobiologie in Bremen angefertigt. 1. Gutachter: Prof. Dr. Rudolf Amann 2. Gutachter: Prof. Dr. Wolfgang Bach 3. Prüfer: Prof. Dr. Ulrich Fischer 4. Prüferin: Dr. Anke Meyerdierks Tag des Promotionskolloquiums: 26.03.2012 1 Table of contents Summary ......................................................................................................................5 Zusammenfassung ......................................................................................................7 List of abbreviations....................................................................................................9 I Introduction.............................................................................................................10 1. Hydrothermal vents ..........................................................................................................10 1.1 Deep-sea hydrothermal vents ........................................................................................11 1.2 Shallow-sea hydrothermal vents
    [Show full text]